From 078808ee9c673930c97272193a28a4491b890050 Mon Sep 17 00:00:00 2001
From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com>
Date: Fri, 21 Feb 2025 13:34:58 +0000
Subject: [PATCH] Added diet_meat in place of dietary_state

---
 docs/jsonBrowser/module.md                    |  2 +-
 .../module/biomaterial/medical_history.json   | 22 +++++--------------
 json_schema/update_log.csv                    |  2 +-
 3 files changed, 7 insertions(+), 19 deletions(-)

diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md
index 0df27071..1b0c2db3 100644
--- a/docs/jsonBrowser/module.md
+++ b/docs/jsonBrowser/module.md
@@ -559,7 +559,7 @@ smoking_status | Whether the individual is actively, was formerly or never consu
 smoking_pack_years | Estimated number of packs (20 cigarettes) smoked per day multiplied by the number of years the individual was smoking. | number | no |  | Smoking pack years |  | 4.55
 years_since_smoking_cessation | If smoking status is 'former', specify the number of years since smoking cessation. | integer | no |  | Years since smoking cessation |  | 12
 nutritional_state | Nutritional state of individual at time of biomaterial collection. | string | no |  | Nutritional state | normal, fasting, feeding tube removed | Should be one of: normal, fasting, or feeding tube removed.
-dietary_state | Dietary state of donor at the time of collection. | string | no |  | Dietary state | gluten_free, fodmap, baby_formula, breastfeeding, elimination, keto, paleo, vegan, vegetarian, omnivore | Should be one of: gluten_free, fodmap, baby_formula, breastfeeding, elimination, keto, paleo, vegan, vegetarian, omnivore.
+diet_meat | Dietary patterns of donor - meat (chicken, seafood, fish, pork, lamb, beef, etc.) consumption versus meat-free diet - at time of sample collection. | boolean | no |  | Meat consumption |  | Should be one of: yes; no. yes stands for donor consumes meat, no stands for donor does not consume meat
 menarche_age | Age at menarche, rounded to nearest whole number. | integer | no |  | Menarche age |  | 10; 11;, 15
 menopause_status | Menopausal status of donor at time of sample collection. | string | no |  | Menopause status | pre-menopausal, peri-menopausal, post-menopausal, post-menopausal (induced) | pre-menopausal; peri-menopausal; post-menopausal; post-menopausal (induced)
 parity | Number of children (full-term pregnancies) the donor has given birth to at time of sample collection. | integer | no |  | Pregnancy - parity |  | 0; 3, 7
diff --git a/json_schema/module/biomaterial/medical_history.json b/json_schema/module/biomaterial/medical_history.json
index bf60570a..d4388a5f 100644
--- a/json_schema/module/biomaterial/medical_history.json
+++ b/json_schema/module/biomaterial/medical_history.json
@@ -68,23 +68,11 @@
             "user_friendly": "Nutritional state",
             "example": "Should be one of: normal, fasting, or feeding tube removed."
         },
-        "dietary_state": {
-            "description": "Dietary state of donor at the time of collection.",
-            "type": "string",
-            "enum": [
-                "gluten_free",
-                "fodmap",
-                "baby_formula",
-                "breastfeeding",
-                "elimination",
-                "keto",
-                "paleo",
-                "vegan",
-                "vegetarian",
-                "omnivore"
-            ],
-            "user_friendly": "Dietary state",
-            "example": "Should be one of: gluten_free, fodmap, baby_formula, breastfeeding, elimination, keto, paleo, vegan, vegetarian, omnivore.",
+        "diet_meat": {
+            "description": "Dietary patterns of donor - meat (chicken, seafood, fish, pork, lamb, beef, etc.) consumption versus meat-free diet - at time of sample collection.",
+            "type": "boolean",
+            "user_friendly": "Meat consumption",
+            "example": "Should be one of: yes; no. yes stands for donor consumes meat, no stands for donor does not consume meat",
             "bionetworks": ["genetic diversity"]
         },
         "menarche_age": {
diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv
index 6ecc6a40..0612334a 100644
--- a/json_schema/update_log.csv
+++ b/json_schema/update_log.csv
@@ -11,7 +11,7 @@ module/biomaterial/human_specific,minor,Added optional place_of_birth_location_c
 module/biomaterial/human_specific,minor,Added optional place_of_birth_location_granular,,
 module/biomaterial/human_specific,minor,Added optional place_of_birth_duration,,
 module/biomaterial/human_specific,minor,Added optional place_of_birth_urbanrural,,
-module/biomaterial/medical_history,minor,Added optional dietary_state,,
+module/biomaterial/medical_history,minor,Added optional diet_meat,,
 module/biomaterial/medical_history,minor,Added optional menarche_age,,
 module/biomaterial/medical_history,minor,Added optional menopause_status,,
 module/biomaterial/medical_history,minor,Added optional parity,,